| simulated annealing |
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER)
MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL.
(1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON
CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON.
SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL
DATABASE
POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 -
1080
AND (1997) J. MAGN. RESON. 125, 171-177)
THE 3D STRUCTURE OF THE COMPLEX OF THE THIRD DNA BINDING
DOMAIN OF HMG-I(Y)
COMPLEXED TO DNA WAS SOLVED BY
MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR
(A) PROTEIN: 31 SEQUENTIAL (|I-J|=1), 2 MEDIUM
RANGE (1 < |I-J| >=5) AND 22 INTRARESIDUE
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL
17 TORSION ANGLE RESTRAINTS
6 THREE-BOND HN-HA AND 3 THREE_BOND COCO COUPLING
CONSTANT RESTRAINTS; 17 (9 CALPHA AND 8 CBETA) 13C
SHIFT RESTRAINTS.
(B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND
33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42
DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS;
136 TORSION ANGLE RESTRAINTS
(C) 34 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(D) 4 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
(E) 28 'REPULSIVE' RESTRAINTS
THE STRUCTURES IN THIS ENTRY ARE THE 35 INDIVIDUAL
SIMULATED ANNEALING STRUCTURES. THE RESTRAINTS REGULARIZED
MEAN STRUCTURE IS FOUND IN PDB ENTRY 2EZF. THE LAST
NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO
MEANING.
RESIDUES 32 - 41 OF THE PROTEIN CORRESPOND TO RESIDUES 79 -
88 OF INTACT HMG-I(Y). |
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